Completely different situation. For one, football teams are hard to directly compare due to the small number of games played and lack of direct competition. Gymnastics? You know exactly how well everyone did against everyone else because their scores are right there. In football there are all kinds of margin for error- from biased pollsters to faulty computer models. Gymnastics? All just have the scores they just got.
Gymnastics has faulty scoring as well. While it's a lot closer to perfect to the BCS, there is still some fault. There's been controversy before in events like this because of judging where the system should be a lot better.
I don't think there is a lot of difference besides like you said, the scoring system. If Wieber didn't make mistakes, she would be in the finals. People would still be complaining in some fashion if the top 24 made it.
It'll be interesting to see the final details of the new championship for college football and see how they go about it.